The world champion aggravated an old injury in practice yesterday and had to reorganise his programme today to avoid putting too much pressure on his wrist.
But after taking a seventh straight pole in qualifying, Stoner said he was not anticipating any problems on race day.
"The injury isn't actually that bad, it's just sometimes when I go into corners if I twist it a little bit the wrong way or the bike shakes, that's when the pain shoots up your arm," Stoner told BBC television.
"It's basically an old injury of mine that's got some small fractures floating around the middle of it, and then when they get trapped in between the bone, it starts sending electric shocks up my arm.
"It's kind of annoying, but if everything goes alright then it doesn't affect me too much."
Although Stoner ultimately took pole at Misano by half a second, he said it had been a challenging session.
"We struggled a little bit in this afternoon's session," he admitted in the post-qualifying press conference.
"We were trying to change the set-up a little bit so we were a bit happier, and the bike that we did the quickest time on this morning just didn't seem to work this afternoon. Then we went back to the other set-up that we had this morning and it seemed to work better, so we're a little confused at the moment.
"But we're really happy with the lap times we're doing on race tyres at the moment. What I was worried about was that we only had time to get two qualifiers in. We always have three and most people have more. But unfortunately when we were testing the race set-up, we ran out of time.
"So I was very happy and very lucky to stay on pole position with only two qualifiers."
Despite his run of poles, Stoner has not won since the Sachsenring in July, having been beaten by Valentino Rossi in a fraught race at Laguna Seca, and having crashed out of lead at Brno a fortnight ago.
He said these events proved that his dominant practice and qualifying form did not necessarily guarantee a race win.
"We've been working quite well all weekend, as at past weekends, but it doesn't always work out," Stoner told the BBC. "So we're just going to have to wait for tomorrow and then try to do the right job."
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